Locus 66

Sequence ID	Eco_1
Location	3,320,058 – 3,320,190
Length	132
Max. P	0.990567

overview

Window 4

Location	3,320,058 – 3,320,177
Length	119
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	96.66
Mean single sequence MFE	-45.87
Consensus MFE	-45.19
Energy contribution	-45.63
Covariance contribution	0.45
Combinations/Pair	1.03
Mean z-score	-4.89
Structure conservation index	0.99
SVM decision value	1.74
SVM RNA-class probability	0.974978
Prediction	RNA

Download alignment: ClustalW | MAF

>Eco_1 3320058 119 + 1
AAAAAAGACGCUUUUCAGCGUCUCUUUUCUGGAAU-UUGGUACCGAGGACGGGACUUGAACCCGUAAGCCCUAUUGGGCACUACCACCUCAAGGUAGCGUGUCUACCAAUUCCACCACCU
((((.(((((((....))))))).)))).((((((-(.......(((((((((.......)))))..((((....)))).......))))..(((((.....))))))))))))...... ( -43.60)
>Sfl_1 1 119 + 1
AAAAGAGACGCUUUUCAGCGUCUCUUUUCUGGAAU-UUGGUACCGAGGACGGGACUUGAACCCGUAAGCCCUAUUGGGCACUACCACCUCAAGGUAGCGUGUCUACCAAUUCCACCACCU
((((((((((((....)))))))))))).((((((-(.......(((((((((.......)))))..((((....)))).......))))..(((((.....))))))))))))...... ( -49.80)
>Sty_1 1 120 + 1
AAAAAAGACGCUUUUCAGCGUCUUUCUUUCGGAAUAUUGGUACCGAGGACGGGACUUGAACCCGUAAGCCCUAUUGGGCACUACCACCUCAAGGUAGCGUGUCUACCAAUUCCACCACCU
...(((((((((....))))))))).....(((((.........(((((((((.......)))))..((((....)))).......))))..(((((.....))))).)))))....... ( -44.20)
>consensus
AAAAAAGACGCUUUUCAGCGUCUCUUUUCUGGAAU_UUGGUACCGAGGACGGGACUUGAACCCGUAAGCCCUAUUGGGCACUACCACCUCAAGGUAGCGUGUCUACCAAUUCCACCACCU
((((((((((((....))))))))))))..(((((.........(((((((((.......)))))..((((....)))).......))))..(((((.....))))).)))))....... (-45.19 = -45.63 +   0.45)

alignment

secondary structure

dotplot

Window 5

Location	3,320,058 – 3,320,177
Length	119
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	96.66
Mean single sequence MFE	-50.20
Consensus MFE	-50.48
Energy contribution	-49.60
Covariance contribution	-0.88
Combinations/Pair	1.11
Mean z-score	-4.43
Structure conservation index	1.01
SVM decision value	2.22
SVM RNA-class probability	0.990567
Prediction	RNA

Download alignment: ClustalW | MAF

>Eco_1 3320058 119 - 1
AGGUGGUGGAAUUGGUAGACACGCUACCUUGAGGUGGUAGUGCCCAAUAGGGCUUACGGGUUCAAGUCCCGUCCUCGGUACCAA-AUUCCAGAAAAGAGACGCUGAAAAGCGUCUUUUUU
......(((((((((((.....((((((.......))))))((((....))))..(((((.......)))))......)))).)-)))))).((((((((((((....)))))))))))) ( -49.90)
>Sfl_1 1 119 - 1
AGGUGGUGGAAUUGGUAGACACGCUACCUUGAGGUGGUAGUGCCCAAUAGGGCUUACGGGUUCAAGUCCCGUCCUCGGUACCAA-AUUCCAGAAAAGAGACGCUGAAAAGCGUCUCUUUU
......(((((((((((.....((((((.......))))))((((....))))..(((((.......)))))......)))).)-)))))).((((((((((((....)))))))))))) ( -52.50)
>Sty_1 1 120 - 1
AGGUGGUGGAAUUGGUAGACACGCUACCUUGAGGUGGUAGUGCCCAAUAGGGCUUACGGGUUCAAGUCCCGUCCUCGGUACCAAUAUUCCGAAAGAAAGACGCUGAAAAGCGUCUUUUUU
......(((((((((((.....((((((.......))))))((((....))))..(((((.......)))))......)))))..)))))).((((((((((((....)))))))))))) ( -48.20)
>consensus
AGGUGGUGGAAUUGGUAGACACGCUACCUUGAGGUGGUAGUGCCCAAUAGGGCUUACGGGUUCAAGUCCCGUCCUCGGUACCAA_AUUCCAGAAAAGAGACGCUGAAAAGCGUCUUUUUU
......(((((((((((.....((((((.......))))))((((....))))..(((((.......)))))......)))))..)))))).((((((((((((....)))))))))))) (-50.48 = -49.60 +  -0.88)

alignment

secondary structure

dotplot

Window 6

Location	3,320,071 – 3,320,190
Length	119
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	97.21
Mean single sequence MFE	-37.03
Consensus MFE	-35.07
Energy contribution	-35.41
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-1.61
Structure conservation index	0.95
SVM decision value	0.12
SVM RNA-class probability	0.591250
Prediction	RNA

Download alignment: ClustalW | MAF

>Eco_1 3320071 119 + 1
UUCAGCGUCUCUUUUCUGGAAU-UUGGUACCGAGGACGGGACUUGAACCCGUAAGCCCUAUUGGGCACUACCACCUCAAGGUAGCGUGUCUACCAAUUCCACCACCUCGGCACGGAUACU
.((.(.(((.......((((((-(.......(((((((((.......)))))..((((....)))).......))))..(((((.....)))))))))))).......))).).)).... ( -36.94)
>Sfl_1 14 119 + 1
UUCAGCGUCUCUUUUCUGGAAU-UUGGUACCGAGGACGGGACUUGAACCCGUAAGCCCUAUUGGGCACUACCACCUCAAGGUAGCGUGUCUACCAAUUCCACCACCUCGGCACGGAUACU
.((.(.(((.......((((((-(.......(((((((((.......)))))..((((....)))).......))))..(((((.....)))))))))))).......))).).)).... ( -36.94)
>Sty_1 14 120 + 1
UUCAGCGUCUUUCUUUCGGAAUAUUGGUACCGAGGACGGGACUUGAACCCGUAAGCCCUAUUGGGCACUACCACCUCAAGGUAGCGUGUCUACCAAUUCCACCACCUCGGCACGGAUACU
.....................((((.((.(((((((((((.......)))))..((((....)))).............(((((.....)))))..........)))))).)).)))).. ( -37.20)
>consensus
UUCAGCGUCUCUUUUCUGGAAU_UUGGUACCGAGGACGGGACUUGAACCCGUAAGCCCUAUUGGGCACUACCACCUCAAGGUAGCGUGUCUACCAAUUCCACCACCUCGGCACGGAUACU
.((.(.(((.......((((((.........(((((((((.......)))))..((((....)))).......))))..(((((.....))))).)))))).......))).).)).... (-35.07 = -35.41 +   0.33)

alignment

secondary structure

dotplot

Window 7

Location	3,320,071 – 3,320,190
Length	119
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	97.21
Mean single sequence MFE	-43.90
Consensus MFE	-42.50
Energy contribution	-42.50
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.09
Structure conservation index	0.97
SVM decision value	1.02
SVM RNA-class probability	0.902366
Prediction	RNA

Download alignment: ClustalW | MAF

>Eco_1 3320071 119 - 1
AGUAUCCGUGCCGAGGUGGUGGAAUUGGUAGACACGCUACCUUGAGGUGGUAGUGCCCAAUAGGGCUUACGGGUUCAAGUCCCGUCCUCGGUACCAA-AUUCCAGAAAAGAGACGCUGAA
((..((.((((((((((((.((....(((((.....)))))(((((.(.((((.((((....)))))))).).))))).))))).)))))))))...-..((.......))))..))... ( -42.90)
>Sfl_1 14 119 - 1
AGUAUCCGUGCCGAGGUGGUGGAAUUGGUAGACACGCUACCUUGAGGUGGUAGUGCCCAAUAGGGCUUACGGGUUCAAGUCCCGUCCUCGGUACCAA-AUUCCAGAAAAGAGACGCUGAA
((..((.((((((((((((.((....(((((.....)))))(((((.(.((((.((((....)))))))).).))))).))))).)))))))))...-..((.......))))..))... ( -42.90)
>Sty_1 14 120 - 1
AGUAUCCGUGCCGAGGUGGUGGAAUUGGUAGACACGCUACCUUGAGGUGGUAGUGCCCAAUAGGGCUUACGGGUUCAAGUCCCGUCCUCGGUACCAAUAUUCCGAAAGAAAGACGCUGAA
((..((.((((((((((((.((....(((((.....)))))(((((.(.((((.((((....)))))))).).))))).))))).)))))))))........(....)...))..))... ( -45.90)
>consensus
AGUAUCCGUGCCGAGGUGGUGGAAUUGGUAGACACGCUACCUUGAGGUGGUAGUGCCCAAUAGGGCUUACGGGUUCAAGUCCCGUCCUCGGUACCAA_AUUCCAGAAAAGAGACGCUGAA
.......((((((((((((.((....(((((.....)))))(((((.(.((((.((((....)))))))).).))))).))))).))))))))).......................... (-42.50 = -42.50 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Fri Dec 1 11:04:58 2006